With auto-advance enabled, the Zoom window relies on a default return height in order to know how far down to move to the next line. With auto-advance disabled, tapping the "New line" icon near the upper right of the Zoom window will also move this far to the next line.
To change this value for a template:
1. From the Library view, tap the Gear icon at the top-right corner > Notebook Templates.
2. Tap Edit in the upper right and then on the template name (where you see three dots).
3. Enter a desired value (in points) in the Height field and tap Save.
Note that this change will only take effect for new notebooks using that template.